PyPI - python-microscopy - Versions diffs - 25.6.5__cp39-cp39-win_amd64.whl - Mend

python-microscopy 25.6.5__cp39-cp39-win_amd64.whl

This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.

Files changed (1277) hide show

PYME/Acquire/ActionManager.py +450 -0
PYME/Acquire/ExecTools.py +235 -0
PYME/Acquire/Hardware/AAOptoelectronics/MDS.py +175 -0
PYME/Acquire/Hardware/AAOptoelectronics/__init__.py +0 -0
PYME/Acquire/Hardware/ARCoptix/__init__.py +0 -0
PYME/Acquire/Hardware/ARCoptix/lcdriver.py +149 -0
PYME/Acquire/Hardware/ARCoptix/lcserver32.py +123 -0
PYME/Acquire/Hardware/AndorIXon/AndorCam.py +1095 -0
PYME/Acquire/Hardware/AndorIXon/AndorControlFrame.py +312 -0
PYME/Acquire/Hardware/AndorIXon/AndorIXon.py +737 -0
PYME/Acquire/Hardware/AndorIXon/__init__.py +27 -0
PYME/Acquire/Hardware/AndorNeo/AndorNeo.py +644 -0
PYME/Acquire/Hardware/AndorNeo/AndorNeoControlFrame.py +161 -0
PYME/Acquire/Hardware/AndorNeo/AndorZyla.py +761 -0
PYME/Acquire/Hardware/AndorNeo/SDK3.py +307 -0
PYME/Acquire/Hardware/AndorNeo/SDK3Cam.py +171 -0
PYME/Acquire/Hardware/AndorNeo/ZylaControlPanel.py +105 -0
PYME/Acquire/Hardware/AndorNeo/__init__.py +22 -0
PYME/Acquire/Hardware/AndorNeo/parseAtdebug.py +46 -0
PYME/Acquire/Hardware/AndorNeo/plotTimings.py +73 -0
PYME/Acquire/Hardware/AndorNeo/testNeo.py +62 -0
PYME/Acquire/Hardware/Camera.py +1199 -0
PYME/Acquire/Hardware/CameraSkeleton.py +642 -0
PYME/Acquire/Hardware/Coherent/OBIS.py +147 -0
PYME/Acquire/Hardware/Coherent/Sapphire.py +162 -0
PYME/Acquire/Hardware/Coherent/__init__.py +0 -0
PYME/Acquire/Hardware/DMDGui.py +198 -0
PYME/Acquire/Hardware/DigiData/DigiData.py +95 -0
PYME/Acquire/Hardware/DigiData/DigiDataClient.py +30 -0
PYME/Acquire/Hardware/DigiData/RemoteDigiData.py +51 -0
PYME/Acquire/Hardware/DigiData/__init__.py +24 -0
PYME/Acquire/Hardware/DigiData/axDD132x.py +348 -0
PYME/Acquire/Hardware/EMCCDTheory.py +41 -0
PYME/Acquire/Hardware/ExciterWheel.py +167 -0
PYME/Acquire/Hardware/FilterWheel.py +184 -0
PYME/Acquire/Hardware/FocCorr.py +106 -0
PYME/Acquire/Hardware/FocCorrR.py +196 -0
PYME/Acquire/Hardware/FrFilter.py +51 -0
PYME/Acquire/Hardware/GCS/GCS_DLL.py +370 -0
PYME/Acquire/Hardware/GCS/__init__.py +0 -0
PYME/Acquire/Hardware/GCS/gcs.py +210 -0
PYME/Acquire/Hardware/HamamatsuDCAM/HamamatsuDCAM.py +662 -0
PYME/Acquire/Hardware/HamamatsuDCAM/HamamatsuORCA.py +602 -0
PYME/Acquire/Hardware/HamamatsuDCAM/Hamamatsu_control_panel.py +54 -0
PYME/Acquire/Hardware/HamamatsuDCAM/__init__.py +23 -0
PYME/Acquire/Hardware/LaserControlFrame.py +160 -0
PYME/Acquire/Hardware/MPBCommunications/MPBCW.py +132 -0
PYME/Acquire/Hardware/MPBCommunications/__init__.py +0 -0
PYME/Acquire/Hardware/Mercury/Mercury.py +269 -0
PYME/Acquire/Hardware/Mercury/PI_Mercury_GCS_DLL.py +857 -0
PYME/Acquire/Hardware/Mercury/__init__.py +22 -0
PYME/Acquire/Hardware/Mercury/mercuryStepper.py +203 -0
PYME/Acquire/Hardware/Mercury/mercuryStepperGCS.py +281 -0
PYME/Acquire/Hardware/NikonTE2000.py +68 -0
PYME/Acquire/Hardware/NikonTi.py +214 -0
PYME/Acquire/Hardware/NikonTiGUI.py +81 -0
PYME/Acquire/Hardware/OrielCornerstone.py +125 -0
PYME/Acquire/Hardware/PM100USB.py +51 -0
PYME/Acquire/Hardware/Piezos/__init__.py +22 -0
PYME/Acquire/Hardware/Piezos/base_piezo.py +108 -0
PYME/Acquire/Hardware/Piezos/offsetPiezo.py +162 -0
PYME/Acquire/Hardware/Piezos/offsetPiezoREST.py +308 -0
PYME/Acquire/Hardware/Piezos/piezo_c867.py +486 -0
PYME/Acquire/Hardware/Piezos/piezo_e255.py +68 -0
PYME/Acquire/Hardware/Piezos/piezo_e662.py +61 -0
PYME/Acquire/Hardware/Piezos/piezo_e709.py +434 -0
PYME/Acquire/Hardware/Piezos/piezo_e816.py +452 -0
PYME/Acquire/Hardware/Piezos/piezo_e816_corr.py +70 -0
PYME/Acquire/Hardware/Piezos/piezo_e816_dll.py +518 -0
PYME/Acquire/Hardware/Piezos/piezo_e816b.py +70 -0
PYME/Acquire/Hardware/Piezos/piezo_pipython_gcs.py +560 -0
PYME/Acquire/Hardware/Piezos/piezo_test.py +55 -0
PYME/Acquire/Hardware/Simulator/EmpiricalHist.py +273 -0
PYME/Acquire/Hardware/Simulator/__init__.py +22 -0
PYME/Acquire/Hardware/Simulator/dSimControl.py +961 -0
PYME/Acquire/Hardware/Simulator/fakeCam.py +651 -0
PYME/Acquire/Hardware/Simulator/fakePiezo.py +95 -0
PYME/Acquire/Hardware/Simulator/fluor.py +336 -0
PYME/Acquire/Hardware/Simulator/illuminate.cp39-win_amd64.dll.a +0 -0
PYME/Acquire/Hardware/Simulator/illuminate.cp39-win_amd64.pyd +0 -0
PYME/Acquire/Hardware/Simulator/illuminate.pyx +93 -0
PYME/Acquire/Hardware/Simulator/lasersliders.py +90 -0
PYME/Acquire/Hardware/Simulator/rend_im.py +446 -0
PYME/Acquire/Hardware/Simulator/setup.py +69 -0
PYME/Acquire/Hardware/Simulator/simcontrol.py +348 -0
PYME/Acquire/Hardware/Simulator/simui_wx.py +794 -0
PYME/Acquire/Hardware/Tango/__init__.py +0 -0
PYME/Acquire/Hardware/Tango/marzhauser_tango.py +583 -0
PYME/Acquire/Hardware/TiLightCrafter.py +388 -0
PYME/Acquire/Hardware/__init__.py +22 -0
PYME/Acquire/Hardware/aotf.py +271 -0
PYME/Acquire/Hardware/arclampshutterpanel.py +71 -0
PYME/Acquire/Hardware/cameraSoftwareBuffer.py +215 -0
PYME/Acquire/Hardware/camera_noise.py +270 -0
PYME/Acquire/Hardware/ccdAdjPanel.py +188 -0
PYME/Acquire/Hardware/ccdCalibrator.py +161 -0
PYME/Acquire/Hardware/cobaltLaser.py +108 -0
PYME/Acquire/Hardware/cobaltLaser561.py +94 -0
PYME/Acquire/Hardware/comports.py +26 -0
PYME/Acquire/Hardware/driftTrackGUI.py +488 -0
PYME/Acquire/Hardware/driftTracking.py +595 -0
PYME/Acquire/Hardware/fakeShutters.py +52 -0
PYME/Acquire/Hardware/focusKeys.py +204 -0
PYME/Acquire/Hardware/focus_locks/__init__.py +0 -0
PYME/Acquire/Hardware/focus_locks/reflection_focus_lock.py +684 -0
PYME/Acquire/Hardware/frZStage.py +117 -0
PYME/Acquire/Hardware/fw102.py +38 -0
PYME/Acquire/Hardware/ids_peak_cam.py +561 -0
PYME/Acquire/Hardware/ioslave.py +305 -0
PYME/Acquire/Hardware/lasers.py +292 -0
PYME/Acquire/Hardware/matchboxLaser.py +58 -0
PYME/Acquire/Hardware/microscope_adapter.py +104 -0
PYME/Acquire/Hardware/mpd_picosecond_delayer.py +395 -0
PYME/Acquire/Hardware/multiview.py +287 -0
PYME/Acquire/Hardware/olympusix81.py +59 -0
PYME/Acquire/Hardware/pco/__init__.py +0 -0
PYME/Acquire/Hardware/pco/pco_cam.py +348 -0
PYME/Acquire/Hardware/pco/pco_edge_42_lt.py +34 -0
PYME/Acquire/Hardware/pco/pco_sdk.py +1645 -0
PYME/Acquire/Hardware/pco/pco_sdk_cam.py +518 -0
PYME/Acquire/Hardware/pco/pco_sdk_cam_control_panel.py +54 -0
PYME/Acquire/Hardware/phoxxLaser.py +199 -0
PYME/Acquire/Hardware/phoxxLaserOLD.py +242 -0
PYME/Acquire/Hardware/priorLumen.py +102 -0
PYME/Acquire/Hardware/priorarclampshutter.py +52 -0
PYME/Acquire/Hardware/setup.py +50 -0
PYME/Acquire/Hardware/spacenav.py +148 -0
PYME/Acquire/Hardware/splitter.py +394 -0
PYME/Acquire/Hardware/thorlabsPiezo.py +98 -0
PYME/Acquire/Hardware/thorlabs_cam.py +136 -0
PYME/Acquire/Hardware/thorlabs_mff_flipper.py +400 -0
PYME/Acquire/Hardware/toptica_ibeam.py +51 -0
PYME/Acquire/Hardware/uc480/AndorControlFrame.py +308 -0
PYME/Acquire/Hardware/uc480/__init__.py +27 -0
PYME/Acquire/Hardware/uc480/uCam480.py +695 -0
PYME/Acquire/Hardware/uc480/uc480.py +189 -0
PYME/Acquire/Hardware/uc480/uc480Deprecated.py +87 -0
PYME/Acquire/Hardware/uc480/uc480_h.py +767 -0
PYME/Acquire/Hardware/uc480/uc480_h_gen.py +62 -0
PYME/Acquire/Hardware/uc480/ucCamControlFrame.py +83 -0
PYME/Acquire/Hardware/ueye.py +702 -0
PYME/Acquire/PYMEAcquire.py +186 -0
PYME/Acquire/Protocols/DMDMFM.py +74 -0
PYME/Acquire/Protocols/__init__.py +22 -0
PYME/Acquire/Protocols/darkCalibrate.py +56 -0
PYME/Acquire/Protocols/dual671_470.py +45 -0
PYME/Acquire/Protocols/dual671_488.py +46 -0
PYME/Acquire/Protocols/gainCal.py +53 -0
PYME/Acquire/Protocols/htsms-cal-psf.py +32 -0
PYME/Acquire/Protocols/htsms-cal-registration.py +52 -0
PYME/Acquire/Protocols/htsms-flow.py +29 -0
PYME/Acquire/Protocols/htsms-staggered.py +31 -0
PYME/Acquire/Protocols/htsms-tile.py +68 -0
PYME/Acquire/Protocols/htsms-two-color.py +29 -0
PYME/Acquire/Protocols/htsms-widefield.py +32 -0
PYME/Acquire/Protocols/paint671.py +61 -0
PYME/Acquire/Protocols/photoconversion.py +52 -0
PYME/Acquire/Protocols/photoconversion2.py +55 -0
PYME/Acquire/Protocols/prebleach488.py +70 -0
PYME/Acquire/Protocols/prebleach490.py +69 -0
PYME/Acquire/Protocols/prebleach561.py +72 -0
PYME/Acquire/Protocols/prebleach561NeomEos2.py +70 -0
PYME/Acquire/Protocols/prebleach561NeomEos2ND1.py +70 -0
PYME/Acquire/Protocols/prebleach642.py +70 -0
PYME/Acquire/Protocols/prebleach671.py +69 -0
PYME/Acquire/Protocols/prebleach671ND1.py +58 -0
PYME/Acquire/Protocols/prebleach671ND2.py +57 -0
PYME/Acquire/Protocols/prebleach671Neo.py +69 -0
PYME/Acquire/Protocols/recover671.py +62 -0
PYME/Acquire/Protocols/sequence642_488.py +85 -0
PYME/Acquire/Protocols/sequence642_561.py +87 -0
PYME/Acquire/Protocols/shiftfield.py +198 -0
PYME/Acquire/Protocols/simul488.py +59 -0
PYME/Acquire/Protocols/simul642.py +63 -0
PYME/Acquire/Protocols/simul642HTSMS.py +63 -0
PYME/Acquire/Protocols/simulPA.py +37 -0
PYME/Acquire/Protocols/simulSIM.py +76 -0
PYME/Acquire/Protocols/simulStep.py +62 -0
PYME/Acquire/Protocols/spdscan.py +178 -0
PYME/Acquire/Protocols/standard470.py +45 -0
PYME/Acquire/Protocols/standard488.py +47 -0
PYME/Acquire/Protocols/standard671.py +48 -0
PYME/Acquire/Protocols/standard671_no532.py +47 -0
PYME/Acquire/Protocols/standardArclamp.py +46 -0
PYME/Acquire/Protocols/strip_tile.py +204 -0
PYME/Acquire/Protocols/tile.py +204 -0
PYME/Acquire/Protocols/tile3D.py +192 -0
PYME/Acquire/Protocols/tile671.py +190 -0
PYME/Acquire/Protocols/tile_triggered.py +189 -0
PYME/Acquire/Scripts/init.py +232 -0
PYME/Acquire/Scripts/init_N1_Ti_Exeter_ZIx.py +374 -0
PYME/Acquire/Scripts/init_N2_Ti_Zyla_lasers.py +290 -0
PYME/Acquire/Scripts/init_Neo.py +266 -0
PYME/Acquire/Scripts/init_NeoSim.py +159 -0
PYME/Acquire/Scripts/init_TIRF.py +232 -0
PYME/Acquire/Scripts/init_TIRF_Neo.py +242 -0
PYME/Acquire/Scripts/init_TIRF_NeoO.py +241 -0
PYME/Acquire/Scripts/init_TIRF_onecam.py +233 -0
PYME/Acquire/Scripts/init_Ti.py +257 -0
PYME/Acquire/Scripts/init_UOA_n.py +256 -0
PYME/Acquire/Scripts/init_UOA_n2.py +246 -0
PYME/Acquire/Scripts/init_Y1.py +249 -0
PYME/Acquire/Scripts/init_Zyla.py +260 -0
PYME/Acquire/Scripts/init_drift_tracking.py +80 -0
PYME/Acquire/Scripts/init_emccd_basic.py +277 -0
PYME/Acquire/Scripts/init_htsms.py +277 -0
PYME/Acquire/Scripts/init_htsms_focus_lock.py +132 -0
PYME/Acquire/Scripts/init_micrpi.py +45 -0
PYME/Acquire/Scripts/init_orca.py +70 -0
PYME/Acquire/Scripts/init_pco.py +49 -0
PYME/Acquire/Scripts/init_rev.py +74 -0
PYME/Acquire/Scripts/init_sim100.py +169 -0
PYME/Acquire/Scripts/init_sim103.py +169 -0
PYME/Acquire/Scripts/init_sim2.py +211 -0
PYME/Acquire/Scripts/init_sim50.py +169 -0
PYME/Acquire/Scripts/init_sim75.py +169 -0
PYME/Acquire/Scripts/init_sim_drift_tracking.py +166 -0
PYME/Acquire/Scripts/init_sim_htsms.py +224 -0
PYME/Acquire/Scripts/init_sim_htsms_n.py +233 -0
PYME/Acquire/Scripts/init_sim_main.py +229 -0
PYME/Acquire/Scripts/init_sim_min.py +197 -0
PYME/Acquire/Scripts/init_sim_rem.py +176 -0
PYME/Acquire/Scripts/init_smi1.py +110 -0
PYME/Acquire/Scripts/init_spectro.py +78 -0
PYME/Acquire/Scripts/init_spim.py +116 -0
PYME/Acquire/Scripts/init_thorcam.py +62 -0
PYME/Acquire/Scripts/init_twophoton.py +112 -0
PYME/Acquire/Scripts/init_uc480.py +262 -0
PYME/Acquire/Scripts/init_ueye.py +261 -0
PYME/Acquire/SpoolController.py +958 -0
PYME/Acquire/Utils/MultiPointScanner.py +80 -0
PYME/Acquire/Utils/__init__.py +13 -0
PYME/Acquire/Utils/failsafe.py +157 -0
PYME/Acquire/Utils/fastTiler.py +153 -0
PYME/Acquire/Utils/pointScanner.py +496 -0
PYME/Acquire/Utils/sarcSpacing.py +86 -0
PYME/Acquire/Utils/strip_tiler.py +93 -0
PYME/Acquire/Utils/tiler.py +464 -0
PYME/Acquire/Utils/vibrationAnalysis.py +65 -0
PYME/Acquire/__init__.py +44 -0
PYME/Acquire/acquire_client.py +90 -0
PYME/Acquire/acquire_server.py +316 -0
PYME/Acquire/acquirebase.py +139 -0
PYME/Acquire/acquiremainframe.py +716 -0
PYME/Acquire/acquirewx.py +61 -0
PYME/Acquire/acquisition_base.py +148 -0
PYME/Acquire/actions.py +209 -0
PYME/Acquire/autofocus.py +54 -0
PYME/Acquire/eventLog.py +95 -0
PYME/Acquire/event_loop.py +119 -0
PYME/Acquire/frameWrangler.py +530 -0
PYME/Acquire/htsms/__init__.py +8 -0
PYME/Acquire/htsms/rule_ui.py +970 -0
PYME/Acquire/htsms/rule_ui_v2.py +573 -0
PYME/Acquire/htsms/tweeter.py +222 -0
PYME/Acquire/microscope.py +1050 -0
PYME/Acquire/positionTracker.py +181 -0
PYME/Acquire/protocol.py +299 -0
PYME/Acquire/protocol_acquisition.py +404 -0
PYME/Acquire/sampleInformation.py +591 -0
PYME/Acquire/sampleInformationDjangoDirect.py +446 -0
PYME/Acquire/setup.py +52 -0
PYME/Acquire/stackSettings.py +295 -0
PYME/Acquire/stage_leveling.py +285 -0
PYME/Acquire/ui/AnalysisSettingsUI.py +184 -0
PYME/Acquire/ui/HDFSpoolFrame.py +584 -0
PYME/Acquire/ui/__init__.py +0 -0
PYME/Acquire/ui/actionUI.py +892 -0
PYME/Acquire/ui/focus_lock_gui.py +149 -0
PYME/Acquire/ui/intensity_trace.py +143 -0
PYME/Acquire/ui/intsliders.py +222 -0
PYME/Acquire/ui/lasersliders.py +329 -0
PYME/Acquire/ui/mpd_picosecond_delay_panel.py +69 -0
PYME/Acquire/ui/multiview_select.py +77 -0
PYME/Acquire/ui/positionUI.py +519 -0
PYME/Acquire/ui/preflight.py +58 -0
PYME/Acquire/ui/scanner_panel.py +41 -0
PYME/Acquire/ui/selectCameraPanel.py +46 -0
PYME/Acquire/ui/seqdialog.py +501 -0
PYME/Acquire/ui/splashScreen.py +175 -0
PYME/Acquire/ui/spool_panel.py +830 -0
PYME/Acquire/ui/tile_panel.py +556 -0
PYME/Acquire/ui/tilesettingsui.py +91 -0
PYME/Acquire/ui/voxelSizeDialog.py +149 -0
PYME/Acquire/webui/__init__.py +36 -0
PYME/Acquire/webui/ipy.py +361 -0
PYME/Acquire/webui/static/css/pyme-bootstrap.css +9908 -0
PYME/Acquire/webui/static/css/pymeacquire.css +85 -0
PYME/Acquire/webui/static/js/pymeacquire.js +375 -0
PYME/Acquire/webui/static/js/pzf.js +95 -0
PYME/Acquire/webui/templates/PYMEAcquire.html +232 -0
PYME/Acquire/webui/templates/login.html +84 -0
PYME/Acquire/webui/templates/xtermpage.html +106 -0
PYME/Acquire/xyztc.py +418 -0
PYME/Acquire/zScanner.py +287 -0
PYME/Analysis/BleachProfile/__init__.py +26 -0
PYME/Analysis/BleachProfile/deMod.py +91 -0
PYME/Analysis/BleachProfile/fitRecover.py +90 -0
PYME/Analysis/BleachProfile/intensProf.py +519 -0
PYME/Analysis/BleachProfile/kinModels.py +507 -0
PYME/Analysis/BleachProfile/rawIntensity.py +227 -0
PYME/Analysis/BleachProfile/rollins.py +555 -0
PYME/Analysis/Colocalisation/__init__.py +27 -0
PYME/Analysis/Colocalisation/colocScaleDep.py +126 -0
PYME/Analysis/Colocalisation/correlationCoeffs.py +198 -0
PYME/Analysis/Colocalisation/distColoc.py +110 -0
PYME/Analysis/Colocalisation/edtColoc.py +191 -0
PYME/Analysis/MetaData.py +278 -0
PYME/Analysis/PSFEst/__init__.py +27 -0
PYME/Analysis/PSFEst/dec.py +283 -0
PYME/Analysis/PSFEst/extractImages.py +316 -0
PYME/Analysis/PSFEst/fit_psf_zernikes.py +194 -0
PYME/Analysis/PSFEst/psfQuality.py +225 -0
PYME/Analysis/PSFGen/__init__.py +40 -0
PYME/Analysis/PSFGen/fourier.py +138 -0
PYME/Analysis/PSFGen/fourierHNA.py +1108 -0
PYME/Analysis/PSFGen/fourierHNA2.py +979 -0
PYME/Analysis/PSFGen/genCRBcurves.py +185 -0
PYME/Analysis/PSFGen/nijboer_zernike.py +79 -0
PYME/Analysis/PSFGen/ps_app.cp39-win_amd64.dll.a +0 -0
PYME/Analysis/PSFGen/ps_app.cp39-win_amd64.pyd +0 -0
PYME/Analysis/PSFGen/test_ps_app.py +24 -0
PYME/Analysis/Tracking/__init__.py +3 -0
PYME/Analysis/Tracking/msd.py +57 -0
PYME/Analysis/Tracking/trackUtils.py +528 -0
PYME/Analysis/Tracking/tracking.py +152 -0
PYME/Analysis/__init__.py +30 -0
PYME/Analysis/_fithelpers.py +161 -0
PYME/Analysis/angleFilter.py +287 -0
PYME/Analysis/annealThresh.py +157 -0
PYME/Analysis/autoencoder_classifier.py +45 -0
PYME/Analysis/binAvg.py +144 -0
PYME/Analysis/composite.py +183 -0
PYME/Analysis/cramerRao.py +259 -0
PYME/Analysis/deTile.py +441 -0
PYME/Analysis/density_filter.py +45 -0
PYME/Analysis/distributed_pyramid.py +426 -0
PYME/Analysis/fiducial_matching.py +220 -0
PYME/Analysis/gen_sCMOS_maps.py +355 -0
PYME/Analysis/graphing_filters.py +311 -0
PYME/Analysis/implicitFilter.py +359 -0
PYME/Analysis/keep_pairs.py +69 -0
PYME/Analysis/optic_flow.py +108 -0
PYME/Analysis/piecewise.py +36 -0
PYME/Analysis/piecewiseMapping.py +304 -0
PYME/Analysis/piezo_movement_correction.py +153 -0
PYME/Analysis/points/DeClump/__init__.py +78 -0
PYME/Analysis/points/DeClump/deClump.cp39-win_amd64.dll.a +0 -0
PYME/Analysis/points/DeClump/deClump.cp39-win_amd64.pyd +0 -0
PYME/Analysis/points/DeClump/deClumpGUI.py +87 -0
PYME/Analysis/points/DeClump/pyDeClump.py +284 -0
PYME/Analysis/points/DeClump/testClump.py +40 -0
PYME/Analysis/points/DistHist/__init__.py +25 -0
PYME/Analysis/points/DistHist/distHist.cp39-win_amd64.dll.a +0 -0
PYME/Analysis/points/DistHist/distHist.cp39-win_amd64.pyd +0 -0
PYME/Analysis/points/DistHist/distHistThreaded.py +71 -0
PYME/Analysis/points/DistHist/setup.py +54 -0
PYME/Analysis/points/EdgeDB/__init__.py +24 -0
PYME/Analysis/points/EdgeDB/edgeDB.cp39-win_amd64.dll.a +0 -0
PYME/Analysis/points/EdgeDB/edgeDB.cp39-win_amd64.pyd +0 -0
PYME/Analysis/points/EdgeDB/edgeTest.py +66 -0
PYME/Analysis/points/EdgeDB/edges.py +102 -0
PYME/Analysis/points/EdgeDB/segment.py +75 -0
PYME/Analysis/points/EdgeDB/setup.py +54 -0
PYME/Analysis/points/QuadTree/QTrend.py +232 -0
PYME/Analysis/points/QuadTree/__init__.py +25 -0
PYME/Analysis/points/QuadTree/pointQT.py +227 -0
PYME/Analysis/points/QuadTree/pointQTF.py +254 -0
PYME/Analysis/points/QuadTree/qtUtils.py +36 -0
PYME/Analysis/points/QuadTree/rendQT.py +118 -0
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PYME/resources/web/static/jstree.min.js +6 -0
PYME/resources/web/static/openSeadragonGL.js +102 -0
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PYME/resources/web/static/openseadragon.min.js +9 -0
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PYME/resources/web/static/shaders/fragment/white.glsl +4 -0
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PYME/resources/web/static/utils.js +3 -0
PYME/resources/web/static/viaWebGL.js +217 -0
PYME/setup.py +109 -0
PYME/setup_exe.py +57 -0
PYME/simulation/__init__.py +0 -0
PYME/simulation/locify.py +319 -0
PYME/simulation/pointsets.py +279 -0
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PYME/ui/about_dlg.py +29 -0
PYME/ui/autoFoldPanel.py +643 -0
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PYME/util/log_verbosity.py +11 -0
PYME/util/mProfile/__init__.py +1 -0
PYME/util/mProfile/colorize_db_t.py +297 -0
PYME/util/mProfile/mProfile.py +164 -0
PYME/util/mProfile/p.py +101 -0
PYME/util/mProfile/tProfile.py +165 -0
PYME/util/pymelauncher.py +47 -0
PYME/util/shmarray/__init__.py +0 -0
PYME/util/shmarray/shmTest.py +74 -0
PYME/util/shmarray/shmarray.py +165 -0
PYME/util/webframework.py +365 -0
PYME/version.py +65 -0
python_microscopy-25.6.5.dist-info/METADATA +68 -0
python_microscopy-25.6.5.dist-info/RECORD +1277 -0
python_microscopy-25.6.5.dist-info/WHEEL +4 -0

PYME/experimental/marching_cubes.py ADDED Viewed

@@ -0,0 +1,811 @@
+import numpy as np
+# MC_EDGES and MC_TRIANGLES from http://paulbourke.net/geometry/polygonise/marchingsource.cpp
+#
+# We assume each cube is arranged in the Euclidean 3-space as follows, where v indicates the vertex number and e
+# indicates the edge number.
+#
+# TODO: Confusingly, the vertex numbering here is different than in PYME.LMVis.layers.octree. This is the correct vertex numbering.
+#
+#           z
+#           ^
+#           |
+#          v4 ----e4----v5
+#          /|           /|
+#         e7|          e5|
+#        /  e8        /  |
+#       v7----e6----v6   e9
+#       |   |        |   |
+#       |  v0----e0--|- v1---> x
+#      e11 /        e10 /
+#       | e3         | e1
+#       |/           |/
+#       v3----e2-----v2
+#      /
+#     y
+#
+# This tells us which row of MC_TRIANGLES to look at based on comparison of isosurface values to grid vertices
+MC_EDGES = np.array([
+    0x000, 0x109, 0x203, 0x30a, 0x406, 0x50f, 0x605, 0x70c, 0x80c, 0x905, 0xa0f, 0xb06, 0xc0a, 0xd03, 0xe09, 0xf00,
+    0x190, 0x099, 0x393, 0x29a, 0x596, 0x49f, 0x795, 0x69c, 0x99c, 0x895, 0xb9f, 0xa96, 0xd9a, 0xc93, 0xf99, 0xe90,
+    0x230, 0x339, 0x033, 0x13a, 0x636, 0x73f, 0x435, 0x53c, 0xa3c, 0xb35, 0x83f, 0x936, 0xe3a, 0xf33, 0xc39, 0xd30,
+    0x3a0, 0x2a9, 0x1a3, 0x0aa, 0x7a6, 0x6af, 0x5a5, 0x4ac, 0xbac, 0xaa5, 0x9af, 0x8a6, 0xfaa, 0xea3, 0xda9, 0xca0,
+    0x460, 0x569, 0x663, 0x76a, 0x066, 0x16f, 0x265, 0x36c, 0xc6c, 0xd65, 0xe6f, 0xf66, 0x86a, 0x963, 0xa69, 0xb60,
+    0x5f0, 0x4f9, 0x7f3, 0x6fa, 0x1f6, 0x0ff, 0x3f5, 0x2fc, 0xdfc, 0xcf5, 0xfff, 0xef6, 0x9fa, 0x8f3, 0xbf9, 0xaf0,
+    0x650, 0x759, 0x453, 0x55a, 0x256, 0x35f, 0x055, 0x15c, 0xe5c, 0xf55, 0xc5f, 0xd56, 0xa5a, 0xb53, 0x859, 0x950,
+    0x7c0, 0x6c9, 0x5c3, 0x4ca, 0x3c6, 0x2cf, 0x1c5, 0x0cc, 0xfcc, 0xec5, 0xdcf, 0xcc6, 0xbca, 0xac3, 0x9c9, 0x8c0,
+    0x8c0, 0x9c9, 0xac3, 0xbca, 0xcc6, 0xdcf, 0xec5, 0xfcc, 0x0cc, 0x1c5, 0x2cf, 0x3c6, 0x4ca, 0x5c3, 0x6c9, 0x7c0,
+    0x950, 0x859, 0xb53, 0xa5a, 0xd56, 0xc5f, 0xf55, 0xe5c, 0x15c, 0x055, 0x35f, 0x256, 0x55a, 0x453, 0x759, 0x650,
+    0xaf0, 0xbf9, 0x8f3, 0x9fa, 0xef6, 0xfff, 0xcf5, 0xdfc, 0x2fc, 0x3f5, 0x0ff, 0x1f6, 0x6fa, 0x7f3, 0x4f9, 0x5f0,
+    0xb60, 0xa69, 0x963, 0x86a, 0xf66, 0xe6f, 0xd65, 0xc6c, 0x36c, 0x265, 0x16f, 0x066, 0x76a, 0x663, 0x569, 0x460,
+    0xca0, 0xda9, 0xea3, 0xfaa, 0x8a6, 0x9af, 0xaa5, 0xbac, 0x4ac, 0x5a5, 0x6af, 0x7a6, 0x0aa, 0x1a3, 0x2a9, 0x3a0,
+    0xd30, 0xc39, 0xf33, 0xe3a, 0x936, 0x83f, 0xb35, 0xa3c, 0x53c, 0x435, 0x73f, 0x636, 0x13a, 0x033, 0x339, 0x230,
+    0xe90, 0xf99, 0xc93, 0xd9a, 0xa96, 0xb9f, 0x895, 0x99c, 0x69c, 0x795, 0x49f, 0x596, 0x29a, 0x393, 0x099, 0x190,
+    0xf00, 0xe09, 0xd03, 0xc0a, 0xb06, 0xa0f, 0x905, 0x80c, 0x70c, 0x605, 0x50f, 0x406, 0x30a, 0x203, 0x109, 0x000
+])
+# Marching cubes triangles. -1 indicates no vertex, 0-11 indicate vertex on edge 0-11. The exact position of a vertex
+# along edge relates to values of vertices on either end of edge.
+MC_TRIANGLES = np.array([
+    [-1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1],
+    [0, 8, 3, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1],
+    [0, 1, 9, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1],
+    [1, 8, 3, 9, 8, 1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1],
+    [1, 2, 10, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1],
+    [0, 8, 3, 1, 2, 10, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1],
+    [9, 2, 10, 0, 2, 9, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1],
+    [2, 8, 3, 2, 10, 8, 10, 9, 8, -1, -1, -1, -1, -1, -1, -1],
+    [3, 11, 2, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1],
+    [0, 11, 2, 8, 11, 0, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1],
+    [1, 9, 0, 2, 3, 11, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1],
+    [1, 11, 2, 1, 9, 11, 9, 8, 11, -1, -1, -1, -1, -1, -1, -1],
+    [3, 10, 1, 11, 10, 3, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1],
+    [0, 10, 1, 0, 8, 10, 8, 11, 10, -1, -1, -1, -1, -1, -1, -1],
+    [3, 9, 0, 3, 11, 9, 11, 10, 9, -1, -1, -1, -1, -1, -1, -1],
+    [9, 8, 10, 10, 8, 11, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1],
+    [4, 7, 8, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1],
+    [4, 3, 0, 7, 3, 4, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1],
+    [0, 1, 9, 8, 4, 7, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1],
+    [4, 1, 9, 4, 7, 1, 7, 3, 1, -1, -1, -1, -1, -1, -1, -1],
+    [1, 2, 10, 8, 4, 7, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1],
+    [3, 4, 7, 3, 0, 4, 1, 2, 10, -1, -1, -1, -1, -1, -1, -1],
+    [9, 2, 10, 9, 0, 2, 8, 4, 7, -1, -1, -1, -1, -1, -1, -1],
+    [2, 10, 9, 2, 9, 7, 2, 7, 3, 7, 9, 4, -1, -1, -1, -1],
+    [8, 4, 7, 3, 11, 2, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1],
+    [11, 4, 7, 11, 2, 4, 2, 0, 4, -1, -1, -1, -1, -1, -1, -1],
+    [9, 0, 1, 8, 4, 7, 2, 3, 11, -1, -1, -1, -1, -1, -1, -1],
+    [4, 7, 11, 9, 4, 11, 9, 11, 2, 9, 2, 1, -1, -1, -1, -1],
+    [3, 10, 1, 3, 11, 10, 7, 8, 4, -1, -1, -1, -1, -1, -1, -1],
+    [1, 11, 10, 1, 4, 11, 1, 0, 4, 7, 11, 4, -1, -1, -1, -1],
+    [4, 7, 8, 9, 0, 11, 9, 11, 10, 11, 0, 3, -1, -1, -1, -1],
+    [4, 7, 11, 4, 11, 9, 9, 11, 10, -1, -1, -1, -1, -1, -1, -1],
+    [9, 5, 4, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1],
+    [9, 5, 4, 0, 8, 3, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1],
+    [0, 5, 4, 1, 5, 0, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1],
+    [8, 5, 4, 8, 3, 5, 3, 1, 5, -1, -1, -1, -1, -1, -1, -1],
+    [1, 2, 10, 9, 5, 4, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1],
+    [3, 0, 8, 1, 2, 10, 4, 9, 5, -1, -1, -1, -1, -1, -1, -1],
+    [5, 2, 10, 5, 4, 2, 4, 0, 2, -1, -1, -1, -1, -1, -1, -1],
+    [2, 10, 5, 3, 2, 5, 3, 5, 4, 3, 4, 8, -1, -1, -1, -1],
+    [9, 5, 4, 2, 3, 11, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1],
+    [0, 11, 2, 0, 8, 11, 4, 9, 5, -1, -1, -1, -1, -1, -1, -1],
+    [0, 5, 4, 0, 1, 5, 2, 3, 11, -1, -1, -1, -1, -1, -1, -1],
+    [2, 1, 5, 2, 5, 8, 2, 8, 11, 4, 8, 5, -1, -1, -1, -1],
+    [10, 3, 11, 10, 1, 3, 9, 5, 4, -1, -1, -1, -1, -1, -1, -1],
+    [4, 9, 5, 0, 8, 1, 8, 10, 1, 8, 11, 10, -1, -1, -1, -1],
+    [5, 4, 0, 5, 0, 11, 5, 11, 10, 11, 0, 3, -1, -1, -1, -1],
+    [5, 4, 8, 5, 8, 10, 10, 8, 11, -1, -1, -1, -1, -1, -1, -1],
+    [9, 7, 8, 5, 7, 9, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1],
+    [9, 3, 0, 9, 5, 3, 5, 7, 3, -1, -1, -1, -1, -1, -1, -1],
+    [0, 7, 8, 0, 1, 7, 1, 5, 7, -1, -1, -1, -1, -1, -1, -1],
+    [1, 5, 3, 3, 5, 7, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1],
+    [9, 7, 8, 9, 5, 7, 10, 1, 2, -1, -1, -1, -1, -1, -1, -1],
+    [10, 1, 2, 9, 5, 0, 5, 3, 0, 5, 7, 3, -1, -1, -1, -1],
+    [8, 0, 2, 8, 2, 5, 8, 5, 7, 10, 5, 2, -1, -1, -1, -1],
+    [2, 10, 5, 2, 5, 3, 3, 5, 7, -1, -1, -1, -1, -1, -1, -1],
+    [7, 9, 5, 7, 8, 9, 3, 11, 2, -1, -1, -1, -1, -1, -1, -1],
+    [9, 5, 7, 9, 7, 2, 9, 2, 0, 2, 7, 11, -1, -1, -1, -1],
+    [2, 3, 11, 0, 1, 8, 1, 7, 8, 1, 5, 7, -1, -1, -1, -1],
+    [11, 2, 1, 11, 1, 7, 7, 1, 5, -1, -1, -1, -1, -1, -1, -1],
+    [9, 5, 8, 8, 5, 7, 10, 1, 3, 10, 3, 11, -1, -1, -1, -1],
+    [5, 7, 0, 5, 0, 9, 7, 11, 0, 1, 0, 10, 11, 10, 0, -1],
+    [11, 10, 0, 11, 0, 3, 10, 5, 0, 8, 0, 7, 5, 7, 0, -1],
+    [11, 10, 5, 7, 11, 5, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1],
+    [10, 6, 5, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1],
+    [0, 8, 3, 5, 10, 6, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1],
+    [9, 0, 1, 5, 10, 6, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1],
+    [1, 8, 3, 1, 9, 8, 5, 10, 6, -1, -1, -1, -1, -1, -1, -1],
+    [1, 6, 5, 2, 6, 1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1],
+    [1, 6, 5, 1, 2, 6, 3, 0, 8, -1, -1, -1, -1, -1, -1, -1],
+    [9, 6, 5, 9, 0, 6, 0, 2, 6, -1, -1, -1, -1, -1, -1, -1],
+    [5, 9, 8, 5, 8, 2, 5, 2, 6, 3, 2, 8, -1, -1, -1, -1],
+    [2, 3, 11, 10, 6, 5, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1],
+    [11, 0, 8, 11, 2, 0, 10, 6, 5, -1, -1, -1, -1, -1, -1, -1],
+    [0, 1, 9, 2, 3, 11, 5, 10, 6, -1, -1, -1, -1, -1, -1, -1],
+    [5, 10, 6, 1, 9, 2, 9, 11, 2, 9, 8, 11, -1, -1, -1, -1],
+    [6, 3, 11, 6, 5, 3, 5, 1, 3, -1, -1, -1, -1, -1, -1, -1],
+    [0, 8, 11, 0, 11, 5, 0, 5, 1, 5, 11, 6, -1, -1, -1, -1],
+    [3, 11, 6, 0, 3, 6, 0, 6, 5, 0, 5, 9, -1, -1, -1, -1],
+    [6, 5, 9, 6, 9, 11, 11, 9, 8, -1, -1, -1, -1, -1, -1, -1],
+    [5, 10, 6, 4, 7, 8, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1],
+    [4, 3, 0, 4, 7, 3, 6, 5, 10, -1, -1, -1, -1, -1, -1, -1],
+    [1, 9, 0, 5, 10, 6, 8, 4, 7, -1, -1, -1, -1, -1, -1, -1],
+    [10, 6, 5, 1, 9, 7, 1, 7, 3, 7, 9, 4, -1, -1, -1, -1],
+    [6, 1, 2, 6, 5, 1, 4, 7, 8, -1, -1, -1, -1, -1, -1, -1],
+    [1, 2, 5, 5, 2, 6, 3, 0, 4, 3, 4, 7, -1, -1, -1, -1],
+    [8, 4, 7, 9, 0, 5, 0, 6, 5, 0, 2, 6, -1, -1, -1, -1],
+    [7, 3, 9, 7, 9, 4, 3, 2, 9, 5, 9, 6, 2, 6, 9, -1],
+    [3, 11, 2, 7, 8, 4, 10, 6, 5, -1, -1, -1, -1, -1, -1, -1],
+    [5, 10, 6, 4, 7, 2, 4, 2, 0, 2, 7, 11, -1, -1, -1, -1],
+    [0, 1, 9, 4, 7, 8, 2, 3, 11, 5, 10, 6, -1, -1, -1, -1],
+    [9, 2, 1, 9, 11, 2, 9, 4, 11, 7, 11, 4, 5, 10, 6, -1],
+    [8, 4, 7, 3, 11, 5, 3, 5, 1, 5, 11, 6, -1, -1, -1, -1],
+    [5, 1, 11, 5, 11, 6, 1, 0, 11, 7, 11, 4, 0, 4, 11, -1],
+    [0, 5, 9, 0, 6, 5, 0, 3, 6, 11, 6, 3, 8, 4, 7, -1],
+    [6, 5, 9, 6, 9, 11, 4, 7, 9, 7, 11, 9, -1, -1, -1, -1],
+    [10, 4, 9, 6, 4, 10, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1],
+    [4, 10, 6, 4, 9, 10, 0, 8, 3, -1, -1, -1, -1, -1, -1, -1],
+    [10, 0, 1, 10, 6, 0, 6, 4, 0, -1, -1, -1, -1, -1, -1, -1],
+    [8, 3, 1, 8, 1, 6, 8, 6, 4, 6, 1, 10, -1, -1, -1, -1],
+    [1, 4, 9, 1, 2, 4, 2, 6, 4, -1, -1, -1, -1, -1, -1, -1],
+    [3, 0, 8, 1, 2, 9, 2, 4, 9, 2, 6, 4, -1, -1, -1, -1],
+    [0, 2, 4, 4, 2, 6, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1],
+    [8, 3, 2, 8, 2, 4, 4, 2, 6, -1, -1, -1, -1, -1, -1, -1],
+    [10, 4, 9, 10, 6, 4, 11, 2, 3, -1, -1, -1, -1, -1, -1, -1],
+    [0, 8, 2, 2, 8, 11, 4, 9, 10, 4, 10, 6, -1, -1, -1, -1],
+    [3, 11, 2, 0, 1, 6, 0, 6, 4, 6, 1, 10, -1, -1, -1, -1],
+    [6, 4, 1, 6, 1, 10, 4, 8, 1, 2, 1, 11, 8, 11, 1, -1],
+    [9, 6, 4, 9, 3, 6, 9, 1, 3, 11, 6, 3, -1, -1, -1, -1],
+    [8, 11, 1, 8, 1, 0, 11, 6, 1, 9, 1, 4, 6, 4, 1, -1],
+    [3, 11, 6, 3, 6, 0, 0, 6, 4, -1, -1, -1, -1, -1, -1, -1],
+    [6, 4, 8, 11, 6, 8, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1],
+    [7, 10, 6, 7, 8, 10, 8, 9, 10, -1, -1, -1, -1, -1, -1, -1],
+    [0, 7, 3, 0, 10, 7, 0, 9, 10, 6, 7, 10, -1, -1, -1, -1],
+    [10, 6, 7, 1, 10, 7, 1, 7, 8, 1, 8, 0, -1, -1, -1, -1],
+    [10, 6, 7, 10, 7, 1, 1, 7, 3, -1, -1, -1, -1, -1, -1, -1],
+    [1, 2, 6, 1, 6, 8, 1, 8, 9, 8, 6, 7, -1, -1, -1, -1],
+    [2, 6, 9, 2, 9, 1, 6, 7, 9, 0, 9, 3, 7, 3, 9, -1],
+    [7, 8, 0, 7, 0, 6, 6, 0, 2, -1, -1, -1, -1, -1, -1, -1],
+    [7, 3, 2, 6, 7, 2, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1],
+    [2, 3, 11, 10, 6, 8, 10, 8, 9, 8, 6, 7, -1, -1, -1, -1],
+    [2, 0, 7, 2, 7, 11, 0, 9, 7, 6, 7, 10, 9, 10, 7, -1],
+    [1, 8, 0, 1, 7, 8, 1, 10, 7, 6, 7, 10, 2, 3, 11, -1],
+    [11, 2, 1, 11, 1, 7, 10, 6, 1, 6, 7, 1, -1, -1, -1, -1],
+    [8, 9, 6, 8, 6, 7, 9, 1, 6, 11, 6, 3, 1, 3, 6, -1],
+    [0, 9, 1, 11, 6, 7, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1],
+    [7, 8, 0, 7, 0, 6, 3, 11, 0, 11, 6, 0, -1, -1, -1, -1],
+    [7, 11, 6, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1],
+    [7, 6, 11, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1],
+    [3, 0, 8, 11, 7, 6, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1],
+    [0, 1, 9, 11, 7, 6, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1],
+    [8, 1, 9, 8, 3, 1, 11, 7, 6, -1, -1, -1, -1, -1, -1, -1],
+    [10, 1, 2, 6, 11, 7, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1],
+    [1, 2, 10, 3, 0, 8, 6, 11, 7, -1, -1, -1, -1, -1, -1, -1],
+    [2, 9, 0, 2, 10, 9, 6, 11, 7, -1, -1, -1, -1, -1, -1, -1],
+    [6, 11, 7, 2, 10, 3, 10, 8, 3, 10, 9, 8, -1, -1, -1, -1],
+    [7, 2, 3, 6, 2, 7, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1],
+    [7, 0, 8, 7, 6, 0, 6, 2, 0, -1, -1, -1, -1, -1, -1, -1],
+    [2, 7, 6, 2, 3, 7, 0, 1, 9, -1, -1, -1, -1, -1, -1, -1],
+    [1, 6, 2, 1, 8, 6, 1, 9, 8, 8, 7, 6, -1, -1, -1, -1],
+    [10, 7, 6, 10, 1, 7, 1, 3, 7, -1, -1, -1, -1, -1, -1, -1],
+    [10, 7, 6, 1, 7, 10, 1, 8, 7, 1, 0, 8, -1, -1, -1, -1],
+    [0, 3, 7, 0, 7, 10, 0, 10, 9, 6, 10, 7, -1, -1, -1, -1],
+    [7, 6, 10, 7, 10, 8, 8, 10, 9, -1, -1, -1, -1, -1, -1, -1],
+    [6, 8, 4, 11, 8, 6, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1],
+    [3, 6, 11, 3, 0, 6, 0, 4, 6, -1, -1, -1, -1, -1, -1, -1],
+    [8, 6, 11, 8, 4, 6, 9, 0, 1, -1, -1, -1, -1, -1, -1, -1],
+    [9, 4, 6, 9, 6, 3, 9, 3, 1, 11, 3, 6, -1, -1, -1, -1],
+    [6, 8, 4, 6, 11, 8, 2, 10, 1, -1, -1, -1, -1, -1, -1, -1],
+    [1, 2, 10, 3, 0, 11, 0, 6, 11, 0, 4, 6, -1, -1, -1, -1],
+    [4, 11, 8, 4, 6, 11, 0, 2, 9, 2, 10, 9, -1, -1, -1, -1],
+    [10, 9, 3, 10, 3, 2, 9, 4, 3, 11, 3, 6, 4, 6, 3, -1],
+    [8, 2, 3, 8, 4, 2, 4, 6, 2, -1, -1, -1, -1, -1, -1, -1],
+    [0, 4, 2, 4, 6, 2, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1],
+    [1, 9, 0, 2, 3, 4, 2, 4, 6, 4, 3, 8, -1, -1, -1, -1],
+    [1, 9, 4, 1, 4, 2, 2, 4, 6, -1, -1, -1, -1, -1, -1, -1],
+    [8, 1, 3, 8, 6, 1, 8, 4, 6, 6, 10, 1, -1, -1, -1, -1],
+    [10, 1, 0, 10, 0, 6, 6, 0, 4, -1, -1, -1, -1, -1, -1, -1],
+    [4, 6, 3, 4, 3, 8, 6, 10, 3, 0, 3, 9, 10, 9, 3, -1],
+    [10, 9, 4, 6, 10, 4, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1],
+    [4, 9, 5, 7, 6, 11, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1],
+    [0, 8, 3, 4, 9, 5, 11, 7, 6, -1, -1, -1, -1, -1, -1, -1],
+    [5, 0, 1, 5, 4, 0, 7, 6, 11, -1, -1, -1, -1, -1, -1, -1],
+    [11, 7, 6, 8, 3, 4, 3, 5, 4, 3, 1, 5, -1, -1, -1, -1],
+    [9, 5, 4, 10, 1, 2, 7, 6, 11, -1, -1, -1, -1, -1, -1, -1],
+    [6, 11, 7, 1, 2, 10, 0, 8, 3, 4, 9, 5, -1, -1, -1, -1],
+    [7, 6, 11, 5, 4, 10, 4, 2, 10, 4, 0, 2, -1, -1, -1, -1],
+    [3, 4, 8, 3, 5, 4, 3, 2, 5, 10, 5, 2, 11, 7, 6, -1],
+    [7, 2, 3, 7, 6, 2, 5, 4, 9, -1, -1, -1, -1, -1, -1, -1],
+    [9, 5, 4, 0, 8, 6, 0, 6, 2, 6, 8, 7, -1, -1, -1, -1],
+    [3, 6, 2, 3, 7, 6, 1, 5, 0, 5, 4, 0, -1, -1, -1, -1],
+    [6, 2, 8, 6, 8, 7, 2, 1, 8, 4, 8, 5, 1, 5, 8, -1],
+    [9, 5, 4, 10, 1, 6, 1, 7, 6, 1, 3, 7, -1, -1, -1, -1],
+    [1, 6, 10, 1, 7, 6, 1, 0, 7, 8, 7, 0, 9, 5, 4, -1],
+    [4, 0, 10, 4, 10, 5, 0, 3, 10, 6, 10, 7, 3, 7, 10, -1],
+    [7, 6, 10, 7, 10, 8, 5, 4, 10, 4, 8, 10, -1, -1, -1, -1],
+    [6, 9, 5, 6, 11, 9, 11, 8, 9, -1, -1, -1, -1, -1, -1, -1],
+    [3, 6, 11, 0, 6, 3, 0, 5, 6, 0, 9, 5, -1, -1, -1, -1],
+    [0, 11, 8, 0, 5, 11, 0, 1, 5, 5, 6, 11, -1, -1, -1, -1],
+    [6, 11, 3, 6, 3, 5, 5, 3, 1, -1, -1, -1, -1, -1, -1, -1],
+    [1, 2, 10, 9, 5, 11, 9, 11, 8, 11, 5, 6, -1, -1, -1, -1],
+    [0, 11, 3, 0, 6, 11, 0, 9, 6, 5, 6, 9, 1, 2, 10, -1],
+    [11, 8, 5, 11, 5, 6, 8, 0, 5, 10, 5, 2, 0, 2, 5, -1],
+    [6, 11, 3, 6, 3, 5, 2, 10, 3, 10, 5, 3, -1, -1, -1, -1],
+    [5, 8, 9, 5, 2, 8, 5, 6, 2, 3, 8, 2, -1, -1, -1, -1],
+    [9, 5, 6, 9, 6, 0, 0, 6, 2, -1, -1, -1, -1, -1, -1, -1],
+    [1, 5, 8, 1, 8, 0, 5, 6, 8, 3, 8, 2, 6, 2, 8, -1],
+    [1, 5, 6, 2, 1, 6, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1],
+    [1, 3, 6, 1, 6, 10, 3, 8, 6, 5, 6, 9, 8, 9, 6, -1],
+    [10, 1, 0, 10, 0, 6, 9, 5, 0, 5, 6, 0, -1, -1, -1, -1],
+    [0, 3, 8, 5, 6, 10, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1],
+    [10, 5, 6, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1],
+    [11, 5, 10, 7, 5, 11, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1],
+    [11, 5, 10, 11, 7, 5, 8, 3, 0, -1, -1, -1, -1, -1, -1, -1],
+    [5, 11, 7, 5, 10, 11, 1, 9, 0, -1, -1, -1, -1, -1, -1, -1],
+    [10, 7, 5, 10, 11, 7, 9, 8, 1, 8, 3, 1, -1, -1, -1, -1],
+    [11, 1, 2, 11, 7, 1, 7, 5, 1, -1, -1, -1, -1, -1, -1, -1],
+    [0, 8, 3, 1, 2, 7, 1, 7, 5, 7, 2, 11, -1, -1, -1, -1],
+    [9, 7, 5, 9, 2, 7, 9, 0, 2, 2, 11, 7, -1, -1, -1, -1],
+    [7, 5, 2, 7, 2, 11, 5, 9, 2, 3, 2, 8, 9, 8, 2, -1],
+    [2, 5, 10, 2, 3, 5, 3, 7, 5, -1, -1, -1, -1, -1, -1, -1],
+    [8, 2, 0, 8, 5, 2, 8, 7, 5, 10, 2, 5, -1, -1, -1, -1],
+    [9, 0, 1, 5, 10, 3, 5, 3, 7, 3, 10, 2, -1, -1, -1, -1],
+    [9, 8, 2, 9, 2, 1, 8, 7, 2, 10, 2, 5, 7, 5, 2, -1],
+    [1, 3, 5, 3, 7, 5, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1],
+    [0, 8, 7, 0, 7, 1, 1, 7, 5, -1, -1, -1, -1, -1, -1, -1],
+    [9, 0, 3, 9, 3, 5, 5, 3, 7, -1, -1, -1, -1, -1, -1, -1],
+    [9, 8, 7, 5, 9, 7, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1],
+    [5, 8, 4, 5, 10, 8, 10, 11, 8, -1, -1, -1, -1, -1, -1, -1],
+    [5, 0, 4, 5, 11, 0, 5, 10, 11, 11, 3, 0, -1, -1, -1, -1],
+    [0, 1, 9, 8, 4, 10, 8, 10, 11, 10, 4, 5, -1, -1, -1, -1],
+    [10, 11, 4, 10, 4, 5, 11, 3, 4, 9, 4, 1, 3, 1, 4, -1],
+    [2, 5, 1, 2, 8, 5, 2, 11, 8, 4, 5, 8, -1, -1, -1, -1],
+    [0, 4, 11, 0, 11, 3, 4, 5, 11, 2, 11, 1, 5, 1, 11, -1],
+    [0, 2, 5, 0, 5, 9, 2, 11, 5, 4, 5, 8, 11, 8, 5, -1],
+    [9, 4, 5, 2, 11, 3, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1],
+    [2, 5, 10, 3, 5, 2, 3, 4, 5, 3, 8, 4, -1, -1, -1, -1],
+    [5, 10, 2, 5, 2, 4, 4, 2, 0, -1, -1, -1, -1, -1, -1, -1],
+    [3, 10, 2, 3, 5, 10, 3, 8, 5, 4, 5, 8, 0, 1, 9, -1],
+    [5, 10, 2, 5, 2, 4, 1, 9, 2, 9, 4, 2, -1, -1, -1, -1],
+    [8, 4, 5, 8, 5, 3, 3, 5, 1, -1, -1, -1, -1, -1, -1, -1],
+    [0, 4, 5, 1, 0, 5, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1],
+    [8, 4, 5, 8, 5, 3, 9, 0, 5, 0, 3, 5, -1, -1, -1, -1],
+    [9, 4, 5, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1],
+    [4, 11, 7, 4, 9, 11, 9, 10, 11, -1, -1, -1, -1, -1, -1, -1],
+    [0, 8, 3, 4, 9, 7, 9, 11, 7, 9, 10, 11, -1, -1, -1, -1],
+    [1, 10, 11, 1, 11, 4, 1, 4, 0, 7, 4, 11, -1, -1, -1, -1],
+    [3, 1, 4, 3, 4, 8, 1, 10, 4, 7, 4, 11, 10, 11, 4, -1],
+    [4, 11, 7, 9, 11, 4, 9, 2, 11, 9, 1, 2, -1, -1, -1, -1],
+    [9, 7, 4, 9, 11, 7, 9, 1, 11, 2, 11, 1, 0, 8, 3, -1],
+    [11, 7, 4, 11, 4, 2, 2, 4, 0, -1, -1, -1, -1, -1, -1, -1],
+    [11, 7, 4, 11, 4, 2, 8, 3, 4, 3, 2, 4, -1, -1, -1, -1],
+    [2, 9, 10, 2, 7, 9, 2, 3, 7, 7, 4, 9, -1, -1, -1, -1],
+    [9, 10, 7, 9, 7, 4, 10, 2, 7, 8, 7, 0, 2, 0, 7, -1],
+    [3, 7, 10, 3, 10, 2, 7, 4, 10, 1, 10, 0, 4, 0, 10, -1],
+    [1, 10, 2, 8, 7, 4, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1],
+    [4, 9, 1, 4, 1, 7, 7, 1, 3, -1, -1, -1, -1, -1, -1, -1],
+    [4, 9, 1, 4, 1, 7, 0, 8, 1, 8, 7, 1, -1, -1, -1, -1],
+    [4, 0, 3, 7, 4, 3, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1],
+    [4, 8, 7, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1],
+    [9, 10, 8, 10, 11, 8, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1],
+    [3, 0, 9, 3, 9, 11, 11, 9, 10, -1, -1, -1, -1, -1, -1, -1],
+    [0, 1, 10, 0, 10, 8, 8, 10, 11, -1, -1, -1, -1, -1, -1, -1],
+    [3, 1, 10, 11, 3, 10, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1],
+    [1, 2, 11, 1, 11, 9, 9, 11, 8, -1, -1, -1, -1, -1, -1, -1],
+    [3, 0, 9, 3, 9, 11, 1, 2, 9, 2, 11, 9, -1, -1, -1, -1],
+    [0, 2, 11, 8, 0, 11, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1],
+    [3, 2, 11, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1],
+    [2, 3, 8, 2, 8, 10, 10, 8, 9, -1, -1, -1, -1, -1, -1, -1],
+    [9, 10, 2, 0, 9, 2, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1],
+    [2, 3, 8, 2, 8, 10, 0, 1, 8, 1, 10, 8, -1, -1, -1, -1],
+    [1, 10, 2, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1],
+    [1, 3, 8, 9, 1, 8, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1],
+    [0, 9, 1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1],
+    [0, 3, 8, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1],
+    [-1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1]
+])
+INTERPOLATION_BITMASK = [1 << n for n in range(12)]
+EDGE_BITMASK = INTERPOLATION_BITMASK[0:8]
+INTERPOLATION_VERTICES = np.array([[0, 1, 2, 3, 4, 5, 6, 7, 0, 1, 2, 3], [1, 2, 3, 0, 5, 6, 7, 4, 4, 5, 6, 7]])
+class MarchingCubes(object):
+    """
+    Base class for marching cubes. Creates a surface triangulation from a set of voxels,
+    represented as 8 vertices each.
+    References
+    ----------
+        * https://www.volume-gfx.com/volume-rendering/marching-cubes/
+        * http://paulbourke.net/geometry/polygonise/
+    """
+    _MC_MAP_MODE_MODIFIED = False #allow us to switch between this and modified marching cubes easily
+    # Datatype for storing triangles created by marching cubes. Mimics STL data structure.
+    # TODO: Add ('normal', '3f4') for real
+    dt = np.dtype([('normal', '3f4'), ('vertex0', '3f4'), ('vertex1', '3f4'), ('vertex2', '3f4')])
+    def __init__(self, isolevel=0):
+        """
+        Initialize the marching cubes algorithm
+        Parameters
+        ----------
+        isolevel : int
+            Threshold determining if vertex lies inside or outside the surface.
+        """
+        self.vertices = None  # A (-1,8,3) set of x,y,z coordinates corresponding to cubes
+        self.values = None  # The corresponding vertex values (-1, 8)
+        self.triangles = None  # The list of triangles
+        self.isolevel = isolevel
+    def cube_index(self, values):
+        """
+        Takes in a set of 8 vertex values (values of v0-v7) and determines if each is above or below the isolevel.
+        Parameters
+        ----------
+        values : np.array
+            Values at the 8 vertices v0-v7 corresponding to if the box is inside/outside the volume.
+        Returns
+        -------
+        indices: int
+            Value to use for lookup in MC_EDGES, MC_TRIANGLES.
+        """
+        # index = 0
+        #
+        # for val in range(len(values)):
+        #     if values[val] < self.isolevel:
+        #         index |= 1 << val
+        #
+        # return index
+        return ((values < self.isolevel) * EDGE_BITMASK).sum(1)
+    def interpolate_vertex(self, v0, v1, v0_value, v1_value, i=None, j0=None, j1=None):
+        """
+        Interpolate triangle vertex along edge formed by v0->v1.
+        Parameters
+        ----------
+        v0, v1 :
+            Vertices of edge v0->v1.
+        v0_value, v1_value:
+            Scalar values at vertices v0, v1. Same values as for vertex_values in edge_index().
+        Returns
+        -------
+        Interpolated vertex of a triangle.
+        """
+        # if np.abs(self.isolevel - v0_value) == 0:
+        #     return v0
+        # if np.abs(self.isolevel - v1_value) == 0:
+        #     return v1
+        # if np.abs(v0_value - v1_value) == 0:
+        #     return v0
+        #
+        # mu = (self.isolevel - v0_value) / (v1_value - v0_value)
+        # p = v0 + mu * (v1 - v0)
+        #
+        # return p
+        # Interpolate
+        mu = (self.isolevel - v0_value) / (v1_value - v0_value)
+        p = v0 + np.multiply(np.repeat(mu, v0.shape[2]).reshape(-1, v0.shape[1], v0.shape[2]), (v1 - v0))
+        # Now take care of mu's div by 0 cases
+        idxs = np.abs(self.isolevel - v0_value) == 0
+        p[idxs, :] = v0[idxs, :]
+        idxs = np.abs(self.isolevel - v1_value) == 0
+        p[idxs, :] = v1[idxs, :]
+        idxs = np.abs(v1_value - v0_value) == 0
+        p[idxs, :] = v0[idxs, :]
+        return p
+    def create_intersection_list(self, edge, vertices, values):
+        """
+        Creates a vertex for each of the 12 edges based on edge_index values.
+        Parameters
+        ----------
+        edge : int
+            MC_EDGES[cube_index]
+        vertices : np.array
+            Cube vertices.
+        values : np.array
+            Cube vertex values.
+        Returns
+        -------
+        vertices of intersection list
+        """
+        # intersection_vertices = np.zeros((12, 3))  # Create one set of intersection vertices, one vertex per edge
+        # if edge & 1:
+        #     intersection_vertices[0] = self.interpolate_vertex(vertices[0], vertices[1], values[0], values[1])
+        # if edge & 2:
+        #     intersection_vertices[1] = self.interpolate_vertex(vertices[1], vertices[2], values[1], values[2])
+        # if edge & 4:
+        #     intersection_vertices[2] = self.interpolate_vertex(vertices[2], vertices[3], values[2], values[3])
+        # if edge & 8:
+        #     intersection_vertices[3] = self.interpolate_vertex(vertices[3], vertices[0], values[3], values[0])
+        # if edge & 16:
+        #     intersection_vertices[4] = self.interpolate_vertex(vertices[4], vertices[5], values[4], values[5])
+        # if edge & 32:
+        #     intersection_vertices[5] = self.interpolate_vertex(vertices[5], vertices[6], values[5], values[6])
+        # if edge & 64:
+        #     intersection_vertices[6] = self.interpolate_vertex(vertices[6], vertices[7], values[6], values[7])
+        # if edge & 128:
+        #     intersection_vertices[7] = self.interpolate_vertex(vertices[7], vertices[4], values[7], values[4])
+        # if edge & 256:
+        #     intersection_vertices[8] = self.interpolate_vertex(vertices[0], vertices[4], values[0], values[4])
+        # if edge & 512:
+        #     intersection_vertices[9] = self.interpolate_vertex(vertices[1], vertices[5], values[1], values[5])
+        # if edge & 1024:
+        #     intersection_vertices[10] = self.interpolate_vertex(vertices[2], vertices[6], values[2], values[6])
+        # if edge & 2048:
+        #     intersection_vertices[11] = self.interpolate_vertex(vertices[3], vertices[7], values[3], values[7])
+        #
+        # return intersection_vertices
+        j0 = INTERPOLATION_VERTICES[0, :]
+        j1 = INTERPOLATION_VERTICES[1, :]
+        v0 = vertices[:, j0]
+        v1 = vertices[:, j1]
+        v0_value = values[:, j0]
+        v1_value = values[:, j1]
+        p = self.interpolate_vertex(v0, v1, v0_value, v1_value, j0=j0, j1=j1)
+        edge_indices = (np.repeat(edge, 12).reshape(edge.shape[0], 12) & INTERPOLATION_BITMASK) == 0
+        p[edge_indices, :] = 0
+        return p
+    def create_triangles(self, intersections, triangles):
+        """
+        Connect the intersection list into triangles.
+        Parameters
+        ----------
+        intersections : np.array
+            Array of edge intersection vertices.
+        triangles : np.array
+            Array of edge indices to form triangles.
+        Returns
+        -------
+        None
+        """
+        # idx = 0
+        #
+        # while triangles[idx] != -1:
+        #     # TODO: currently adds a normal of [1, 1, 1]
+        #     self.triangles.append(([0, 0, 0], intersections[triangles[idx]].tolist(),
+        #                            intersections[triangles[idx+1]].tolist(), intersections[triangles[idx+2]].tolist(),
+        #                            0))
+        #     idx += 3
+        idxs = np.array(np.where(triangles[:, 0] != -1)).reshape(-1)
+        triangles_pruned = triangles[idxs].flatten()
+        idxs = np.repeat(idxs, triangles.shape[1])[triangles_pruned != -1]
+        triangles_pruned = triangles_pruned[triangles_pruned != -1]
+        triangles_returned = intersections[idxs, triangles_pruned].reshape(int(idxs.shape[0] // 3), 3, 3)
+        normals = np.cross((triangles_returned[:, 2] - triangles_returned[:, 1]),
+                           (triangles_returned[:, 0] - triangles_returned[:, 1]))
+        triangles_stl = np.zeros(triangles_returned.shape[0], dtype=self.dt)
+        triangles_stl['vertex0'] = triangles_returned[:, 0, :]
+        triangles_stl['vertex1'] = triangles_returned[:, 1, :]
+        triangles_stl['vertex2'] = triangles_returned[:, 2, :]
+        triangles_stl['normal'] = normals
+        self.triangles = triangles_stl
+        return self.triangles
+    def set_vertices(self, vertices, values):
+        """
+        Set input vertices (self.vertices) & set values (self.values) based on input vertices to use for isosurface
+        extraction.
+        * self.vertices is a (-1,8,3) set of x,y,z coordinates corresponding to cubes
+        * self.values are the corresponding vertex values (-1, 8)
+        overridden in derived classes
+        """
+        self.vertices = vertices
+        self.values = values
+    def export_triangles(self):
+        """
+        Return the list of triangles as a dtyped np array for use in triangular rendering.
+        Returns
+        -------
+        triangles : np.array
+            Array of triangles of type self.dt
+        """
+        return self.triangles
+    def march(self, return_triangles=True, **kwargs):
+        """
+        March over the input vertices.
+        Parameters
+        ----------
+        return_triangles : bool
+            Return the list of triangles post-march or nah?
+        Returns
+        -------
+        Optionally, an array of triangles after marching.
+        """
+        cube_index = self.cube_index(self.values)
+        #we don't need to calculate anything if all vertices of a cube are above or below the threshold
+        mask = ~((cube_index == 0) | (cube_index == 0xFF))
+        edge = MC_EDGES[cube_index[mask]]
+        intersections = self.create_intersection_list(edge, self.vertices[mask,:,:], self.values[mask,:])
+        triangles = MC_TRIANGLES[cube_index[mask]]
+        self.create_triangles(intersections, triangles)
+        # for v_index in range(self.vertices.shape[0]):
+        #     values = self.values[v_index, :]
+        #     cube_index = self.cube_index(values)
+        #
+        #     edge = MC_EDGES[cube_index]
+        #     if edge == 0:
+        #         continue
+        #
+        #     vertices = self.vertices[v_index, :, :]
+        #
+        #     intersections = self.create_intersection_list(edge, vertices, values)
+        #     triangles = MC_TRIANGLES[cube_index]
+        #     self.create_triangles(intersections, triangles)
+        if return_triangles:
+            return self.export_triangles()
+class RasterMarchingCubes(MarchingCubes):
+    """
+    Marching cubes with some optimisations data on a regular grid
+    """
+    v_offsets = np.array([[0,0,0],
+                          [1,0,0],
+                          [1,1,0],
+                          [0,1,0],
+                          [0, 0, 1],
+                          [1, 0, 1],
+                          [1, 1, 1],
+                          [0, 1, 1]])
+    def __init__(self, image, isolevel=0, voxelsize=(1.,1.,1.)):
+        """
+        Initialize the marching cubes algorithm
+        Parameters
+        ----------
+        isolevel : int
+            Threshold determining if vertex lies inside or outside the surface.
+        """
+        self.image = image.squeeze().astype('f')
+        self.voxelsize = voxelsize
+        self.triangles = None  # The list of triangles
+        self.isolevel = isolevel
+    def cube_index(self):
+        """
+        Takes in a set of 8 vertex values (values of v0-v7) and determines if each is above or below the isolevel.
+        Parameters
+        ----------
+        values : np.array
+            Values at the 8 vertices v0-v7 corresponding to if the box is inside/outside the volume.
+        Returns
+        -------
+        indices: int
+            Value to use for lookup in MC_EDGES, MC_TRIANGLES.
+        """
+        imm = self.image < self.isolevel
+        res = (imm[:-1,:-1,:-1] << 0) + \
+              (imm[1:, :-1,:-1] << 1) + \
+              (imm[1:, 1:, :-1] << 2) + \
+              (imm[:-1, 1:, :-1] << 3) + \
+              (imm[:-1, :-1, 1:] << 4) + \
+              (imm[1:, :-1, 1:] << 5) + \
+              (imm[1:, 1:, 1:] << 6) + \
+              (imm[:-1, 1:, 1:] << 7)
+        return res
+    def gen_vertices_and_vals(self, cube_mask):
+        coords = np.argwhere(cube_mask)[:,None,:] + self.v_offsets[None,:,:]
+        values = self.image[coords[:,:,0], coords[:,:,1], coords[:,:,2]]
+        #print(coords.shape, values.shape)
+        return coords.astype('f')*np.array(self.voxelsize)[None,None,:], values
+    def march(self, return_triangles=True, **kwargs):
+        """
+        March over the input vertices.
+        Parameters
+        ----------
+        return_triangles : bool
+            Return the list of triangles post-march or nah?
+        Returns
+        -------
+        Optionally, an array of triangles after marching.
+        """
+        cube_index = self.cube_index()
+        #print(cube_index.dtype, cube_index.max(), cube_index.min())
+        #we don't need to calculate anything if all vertices of a cube are above or below the threshold
+        mask = ~((cube_index == 0) | (cube_index == 0xFF))
+        #print(self.image.shape, cube_index.shape, mask.shape, mask.sum())
+        cube_index = cube_index[mask].ravel()
+        edge = MC_EDGES[cube_index]
+        intersections = self.create_intersection_list(edge, *self.gen_vertices_and_vals(mask))
+        triangles = MC_TRIANGLES[cube_index]
+        self.create_triangles(intersections, triangles)
+        if return_triangles:
+            return self.export_triangles()
+def generate_sphere_voxels(radius=10):
+    """
+    Generate a set of voxels representing a sphere to test marching cubes.
+    Parameters
+    ----------
+    radius : int
+        Radius of the 3D sphere.
+    Returns
+    -------
+    vertices : np.array
+        The vertices of the sphere voxels, shape (-1, 8, 3).
+    values : np.array
+        The corresponding values at the vertices coordinates, shape (-1, 8).
+    """
+    cube_width = 1  # voxel step size
+    vertices = []
+    values = []
+    for z in range(2 * radius):
+        for y in range(2 * radius):
+            for x in range(2 * radius):
+                # Default to we're outside the sphere
+                v0 = v1 = v2 = v3 = v4 = v5 = v6 = v7 = 0
+                vertices.append([(x, y, z), (x + cube_width, y, z),
+                                 (x + cube_width, y + cube_width, z),
+                                 (x, y + cube_width, z),
+                                 (x, y, z + cube_width),
+                                 (x + cube_width, y, z + cube_width),
+                                 (x + cube_width, y + cube_width, z + cube_width),
+                                 (x, y + cube_width, z + cube_width)
+                                 ])
+                if ((x - radius) ** 2 + (y - radius) ** 2 +
+                        (z - radius) ** 2) <= radius ** 2 / 4:
+                    v0 = 1
+                if ((x + cube_width - radius) ** 2 + (y - radius) ** 2 +
+                        (z - radius) ** 2) <= radius ** 2 / 4:
+                    v1 = 1
+                if ((x + cube_width - radius) ** 2 + (y + cube_width - radius) ** 2 +
+                        (z - radius) ** 2) <= radius ** 2 / 4:
+                    v2 = 1
+                if ((x - radius) ** 2 + (y + cube_width - radius) ** 2 +
+                        (z - radius) ** 2) <= radius ** 2 / 4:
+                    v3 = 1
+                if ((x - radius) ** 2 + (y - radius) ** 2 +
+                        (z + cube_width - radius) ** 2) <= radius ** 2 / 4:
+                    v4 = 1
+                if ((x + cube_width - radius) ** 2 + (y - radius) ** 2 +
+                        (z + cube_width - radius) ** 2) <= radius ** 2 / 4:
+                    v5 = 1
+                if ((x + cube_width - radius) ** 2 + (y + cube_width - radius) ** 2 +
+                        (z + cube_width - radius) ** 2) <= radius ** 2 / 4:
+                    v6 = 1
+                if ((x - radius) ** 2 + (y + cube_width - radius) ** 2 +
+                        (z + cube_width - radius) ** 2) <= radius ** 2 / 4:
+                    v7 = 1
+                values.append([v0, v1, v2, v3, v4, v5, v6, v7])
+    return np.array(vertices), np.array(values)
+def generate_sphere_image(radius=10):
+    """Generate a 3D volume image of a sphere. Note that the intensity tapers at the radius (rather than ending abruptly)
+    so that marching cubes can do it's thing properly"""
+    X, Y, Z = np.mgrid[(-1.5*radius):(1.5*radius):1.0, (-1.5*radius):(1.5*radius):1.0, (-1.5*radius):(1.5*radius):1.0]
+    # Uncomment to create sphere missing a top
+    # X += radius/2
+    # Y += radius/5
+    # Z += radius/5
+    R2 = np.sqrt(X*X + Y*Y + Z*Z)
+    S = np.tanh(R2 - radius)
+    return S
+def image_to_vertex_values(im, voxelsize=1.0):
+    """
+    Translate a volume image into a series of vertices and values for marching cubes.
+    Note: this is for debugging and uses ~32x the memory that is required to store the image. In practical applications
+    it might be more efficient to generate these vertices and values inside a modified version of the marching cubes code
+    Parameters
+    ----------
+    im
+    voxelsize
+    Returns
+    -------
+    """
+    if np.isscalar(voxelsize):
+        V = voxelsize*np.mgrid[0:im.shape[0], 0:im.shape[1], 0:im.shape[2]]
+    else:
+        V = np.array(voxelsize)[:,None,None,None]*np.mgrid[0:im.shape[0], 0:im.shape[1], 0:im.shape[2]]
+    def _rs(v):
+        return v.reshape(3, -1).T.reshape(-1, 1, 3)
+    def _rs_i(i):
+        return i.ravel().reshape(-1, 1)
+    vertices = np.concatenate([_rs(V[:, :-1, :-1, :-1]),
+                               _rs(V[:, 1:, :-1, :-1]),
+                               _rs(V[:, 1:, 1:, :-1]),
+                               _rs(V[:, :-1, 1:, :-1]),
+                               _rs(V[:, :-1, :-1, 1:]),
+                               _rs(V[:, 1:, :-1, 1:]),
+                               _rs(V[:, 1:, 1:, 1:]),
+                               _rs(V[:, :-1, 1:, 1:])], 1)
+    values = np.concatenate([_rs_i(im[:-1, :-1, :-1]),
+                               _rs_i(im[1:, :-1, :-1]),
+                               _rs_i(im[1:, 1:, :-1]),
+                               _rs_i(im[:-1, 1:, :-1]),
+                               _rs_i(im[:-1, :-1, 1:]),
+                               _rs_i(im[1:, :-1, 1:]),
+                               _rs_i(im[1:, 1:, 1:]),
+                               _rs_i(im[:-1, 1:, 1:])], 1)
+    return vertices, values